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Party officials said a panel "unanimously" recommended the decision.
Simon Danczuk, who has been serving as an independent MP since his suspension in December, had said he "expected" to be the party's candidate on 8 June.
It follows news his former wife Karen was not selected as Labour candidate for Bury North.
A Labour party spokesperson said: "After considering the case of Simon Danczuk in detail and speaking to him in an interview, the Labour Party's NEC endorsement panel today unanimously recommended that he should not be endorsed as a Labour candidate.
"He will not be able to stand as a Labour candidate in any constituency at the general election."
Mr Danczuk is yet to comment.
The 50-year-old who held the Rochdale seat since 2010 was suspended after The Sun alleged he exchanged explicit messages with a 17-year-old girl.
On Twitter, the Rochdale MP said the story was "not entirely accurate" but referred to "an extremely low point" in his life.
The Labour Party has also chosen James Frith instead of Karen Danczuk to stand for Bury North, which is currently held by Conservative David Nuttall, in the snap general election.